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- PDB-7b61: Crystal structure of MurE from E.coli in complex with Z57299526 -

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Basic information

Entry
Database: PDB / ID: 7b61
TitleCrystal structure of MurE from E.coli in complex with Z57299526
ComponentsUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
KeywordsBIOSYNTHETIC PROTEIN / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2 / 6-diaminopimelate ligase cell wall biosynthesis ligase drug target / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily ...UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / ISOPROPYL ALCOHOL / (S)-N-(1-cyclopropylethyl)-6-methylpicolinamide / (R)-N-(1-cyclopropylethyl)-6-methylpicolinamide / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKoekemoer, L. / Steindel, M. / Fairhead, M. / Talon, R. / Douangamath, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of MurE from E.coli
Authors: Koekemoer, L. / Steindel, M. / Fairhead, M. / Talon, R. / Douangamath, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Krojer, T.
History
DepositionDec 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,50713
Polymers106,9872
Non-polymers1,52011
Water6,377354
1
A: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2146
Polymers53,4941
Non-polymers7215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2927
Polymers53,4941
Non-polymers7996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.150, 58.240, 74.030
Angle α, β, γ (deg.)96.93, 91.27, 105.20
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase / Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso- ...Meso-A2pm-adding enzyme / Meso-diaminopimelate-adding enzyme / UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase / UDP-MurNAc-tripeptide synthetase / UDP-N-acetylmuramyl-tripeptide synthetase


Mass: 53493.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: murE, b0085, JW0083 / Plasmid: pNIC28-Bsa4
Details (production host): N-terminal His6-tag -Twin-Strep-tag II -TEV-cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): -R3-Rosetta
References: UniProt: P22188, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase

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Non-polymers , 6 types, 365 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-SYQ / (S)-N-(1-cyclopropylethyl)-6-methylpicolinamide / ~{N}-[(1~{S})-1-cyclopropylethyl]-6-methyl-pyridine-2-carboxamide


Mass: 204.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-T3Z / (R)-N-(1-cyclopropylethyl)-6-methylpicolinamide / ~{N}-[(1~{R})-1-cyclopropylethyl]-6-methyl-pyridine-2-carboxamide


Mass: 204.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N2O
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M citrate pH 5.5 17% PEG4K 22% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.57→73.38 Å / Num. obs: 124106 / % possible obs: 94.9 % / Redundancy: 1.7 % / CC1/2: 0.997 / Net I/σ(I): 7.5
Reflection shellResolution: 1.57→1.65 Å / Num. unique obs: 18002 / CC1/2: 0.427

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B53

7b53


Resolution: 1.65→56.09 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.669 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22694 5464 5.1 %RANDOM
Rwork0.19323 ---
obs0.19495 102513 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20.99 Å2-0.13 Å2
2--0.6 Å20.77 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→56.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 106 354 7696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0187592
X-RAY DIFFRACTIONr_bond_other_d0.0010.027104
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.88910328
X-RAY DIFFRACTIONr_angle_other_deg1.2212.92416393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38823.945327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.611151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.471555
X-RAY DIFFRACTIONr_chiral_restr0.1090.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021516
X-RAY DIFFRACTIONr_mcbond_it2.9093.3443903
X-RAY DIFFRACTIONr_mcbond_other2.9093.3443904
X-RAY DIFFRACTIONr_mcangle_it3.9375.0074902
X-RAY DIFFRACTIONr_mcangle_other3.9365.0064895
X-RAY DIFFRACTIONr_scbond_it3.9833.8553689
X-RAY DIFFRACTIONr_scbond_other3.9833.8553690
X-RAY DIFFRACTIONr_scangle_other5.7965.6055413
X-RAY DIFFRACTIONr_long_range_B_refined7.22540.8798214
X-RAY DIFFRACTIONr_long_range_B_other7.21740.7638161
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 346 -
Rwork0.321 7498 -
obs--94.93 %

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